seqtree 0.6.0 — the corrected MJ A-N contact energy

Fixed

• structural scored A–N contacts as if they did not interact, because the source table is
  corrupted there. The Miyazawa–Jernigan A–N contact energy was transcribed as 0.00 — the
  generator's comment excused it as a pair the source left unlisted. It is not unlisted. In
  MJ_Keskin_potentials.csv the lower triangle runs A-A, R-A, R-R, [N-A], N-R, …, and
  the N-A slot reads V,1 (mirrored 1,V), where 1 is a mangled residue symbol. The true
  value is 0.15. It is not a stray duplicate of V-N either — the V row separately lists
  N = 0.12.

  Substituting 0.00 for 0.15 understated A's interaction strength and overstated N's
  (q(A) −0.04100 → −0.03350, q(N) +0.04350 → +0.05100). Since structural is rank-1 by
  construction — every cell is a function of the 20 per-residue strengths — this moved the
  strong→weak ordering that the matrix exists to encode, swapping N and P:
  FWCLYMIVHGATNPRSQDEK → FWCLYMIVHGATPNRSQDEK.

  Four cells of the 24×24 grid change: A-W/W-A 6 → 5, and B-C/C-B 4 → 3 (B is
  mean(N, D), so N's shift carries into it). Scores from structural() change for sequences
  containing A, W, or B; all other matrices are untouched. N and P were near-tied, which is why
  a real correction to the ordering moves so few cells.

• The same comment claimed the source is "near- but not perfectly symmetric". It is perfectly
  symmetric — 0 asymmetric directed pairs across all 400. The symmetrisation in
  structural_grid() is a no-op guard, not a repair, and is now documented as such.